The face-to-face took place on June 29 and lasted nearly three hours, according to Russian government spokesman Dmitry Peskov.
Months of tension between Prigozhin and Putin came to a head when the Wagner troops seized the Russian city of Rostov-on-Don and marched on Moscow on June 24.
However, a deal was brokered which saw Prigozhin call off his assault and reportedly agree to live in neighbouring Belarus, although his current whereabouts are unknown.
A total of 35 people attended the Kremlin talks, including “all the commanders of the military detachments”, the spokesman said.
“The president gave an assessment of the company’s actions on the front,” he added.
“He also gave assessment to the June 24 events. Putin listened to the commanders’ explanations and suggested variants of their future employment and their future use in combat.”
Prigozhin also told Putin that the Wagner Group fully supports him, the spokesman said.
It is all a far cry from the run-up to the mutiny attempt, when Prigozhin accused Moscow of killing 2,000 of his men and warned that those responsible would be “punished”.
In a televised address, Putin accused the Wagner Group of “a stab in the back” after they had initially fought alongside his troops in Ukraine.
He said: “Russia will defend itself and repel this move. We are fighting for the life and security of our citizens.”
A notorious Russian general with links to the Wagner Group has not been seen in public since the failed mutiny.